Package picard.analysis.directed
Class HsMetricCollector
- java.lang.Object
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- picard.metrics.MultiLevelCollector<BEAN,HKEY,htsjdk.samtools.SAMRecord>
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- picard.metrics.SAMRecordMultiLevelCollector<METRIC_TYPE,Integer>
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- picard.analysis.directed.TargetMetricsCollector<HsMetrics>
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- picard.analysis.directed.HsMetricCollector
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public class HsMetricCollector extends TargetMetricsCollector<HsMetrics>
Calculates HS metrics for a given SAM or BAM file. Requires the input of a list of target intervals and a list of bait intervals. Can be invoked either on an entire iterator of SAMRecords or be passed SAMRecords one at a time.
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Nested Class Summary
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Nested classes/interfaces inherited from class picard.analysis.directed.TargetMetricsCollector
TargetMetricsCollector.Coverage, TargetMetricsCollector.PerUnitTargetMetricCollector
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Field Summary
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Fields inherited from class picard.analysis.directed.TargetMetricsCollector
NEAR_PROBE_DISTANCE_DEFAULT
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Fields inherited from class picard.metrics.MultiLevelCollector
UNKNOWN
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Constructor Summary
Constructors Constructor Description HsMetricCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, htsjdk.samtools.reference.ReferenceSequenceFile refFile, File perTargetCoverage, File perBaseCoverage, htsjdk.samtools.util.IntervalList targetIntervals, htsjdk.samtools.util.IntervalList probeIntervals, String probeSetName, int nearProbeDistance, int minimumMappingQuality, int minimumBaseQuality, boolean clipOverlappingReads, boolean noSideEffects, boolean includeIndels, int coverageCap, int sampleSize)
HsMetricCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, htsjdk.samtools.reference.ReferenceSequenceFile refFile, File perTargetCoverage, File perBaseCoverage, htsjdk.samtools.util.IntervalList targetIntervals, htsjdk.samtools.util.IntervalList probeIntervals, String probeSetName, int nearProbeDistance, int minimumMappingQuality, int minimumBaseQuality, boolean clipOverlappingReads, int coverageCap, int sampleSize)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description HsMetrics
convertMetric(TargetMetrics targetMetrics)
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Methods inherited from class picard.analysis.directed.TargetMetricsCollector
getBaseQualityHistogram, getDepthHistogram, getNearProbeDistance, getNumBasesPassingMinimumBaseQuality, makeAllReadCollector, makeChildCollector, reflectiveCopy, setNearProbeDistance, setNoSideEffects
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Methods inherited from class picard.metrics.SAMRecordMultiLevelCollector
makeArg
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Methods inherited from class picard.metrics.MultiLevelCollector
acceptRecord, addAllLevelsToFile, finish, getAllReadsCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup
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Constructor Detail
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HsMetricCollector
public HsMetricCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, htsjdk.samtools.reference.ReferenceSequenceFile refFile, File perTargetCoverage, File perBaseCoverage, htsjdk.samtools.util.IntervalList targetIntervals, htsjdk.samtools.util.IntervalList probeIntervals, String probeSetName, int nearProbeDistance, int minimumMappingQuality, int minimumBaseQuality, boolean clipOverlappingReads, int coverageCap, int sampleSize)
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HsMetricCollector
public HsMetricCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, htsjdk.samtools.reference.ReferenceSequenceFile refFile, File perTargetCoverage, File perBaseCoverage, htsjdk.samtools.util.IntervalList targetIntervals, htsjdk.samtools.util.IntervalList probeIntervals, String probeSetName, int nearProbeDistance, int minimumMappingQuality, int minimumBaseQuality, boolean clipOverlappingReads, boolean noSideEffects, boolean includeIndels, int coverageCap, int sampleSize)
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Method Detail
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convertMetric
public HsMetrics convertMetric(TargetMetrics targetMetrics)
- Specified by:
convertMetric
in classTargetMetricsCollector<HsMetrics>
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